We are using an HPC with Slurm as the job scheduler and Singularity for containerization. We want to create an environment module for nf-core. What is the most effective way to install and run offline nf-core pipelines? Do you have any example scripts or implementation guidelines (at institutional level)?

I do not think that there is a one-size fits all solution to your problem. It depends on how many pipelines you wish to run and how frequently you want to update. Will everybody run the same revision or do you need to support multiple? Do you need to do formal validations and verifications?

nf-core pipelines download

and nf-core configs are a good place to start. > We want to create an environment module for nf-core If you have somebody in your team with the permissions to do that, it could work. Our HPC admins told us to not rely on the module system, since they won’t update it frequently. The latest version in the module system for us is e.g.

Nextflow 22.10

I believe? We use conda environments that contain all the required software and configuration, which we version and call “deployments”. The scripts for that can be found here, but are highly custom, so will probably require so much work to adapt, that starting from scratch is probably the better choice.

thank you :) I asked our system admin and i am waiting for answer…